David I Smith
Mayo Clinic, USA
Title: Mate-Pair Sequencing (MP-Seq) as a powerful clinical tool for the management of cancer patients
Biography
Biography: David I Smith
Abstract
Advances in DNA sequencing based upon massively parallel sequencing (Next Generation Sequencing- NGS) have dramatically increased sequence output. The Illumina sequencing platform is now capable of producing billions of simultaneous DNA sequences and this facilitates a number of different ways of characterizing nucleic acids. The most powerful use of NGS is for whole genome sequencing (WGS), but there are a number of limitations of utilizing WGS for the management of cancer patients, including the total cost and difficulties in interpreting the resulting data. A powerful alternative to WGS is the construction of mate-pair libraries and the sequencing of libraries of DNA fragments that were originally kilobases apart. We have been utilizing MP-Seq to characterize oropharyngeal squamous cell carcinomas (OPSCC) which are cancers that are increasingly caused by human papillomavirus. We will describe how MP-Seq can characterize the physical status of HPV in HPV-positive OPSCCs and the clinical significance of this characterization. This work has demonstrated that HPV plays different roles in the development of OPSCCs and many of these are quite distinct from HPVs role in the development of cervical cancer. In addition, MP-Seq can characterize genomic changes in each cancer and these can be used to develop cancer-specific markers, which can be used to monitor an individual patient response to therapy. Thus, MP-Seq could be a powerful and yet affordable tool that can be used as a clinical tool for the management of cancer patients.